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- PDB-3rzp: Crystal Structure of the C194A mutant of 7-cyano-7-deazaguanine r... -

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Open data


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Basic information

Entry
Database: PDB / ID: 3rzp
TitleCrystal Structure of the C194A mutant of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with preQ1
ComponentsNADPH-dependent 7-cyano-7-deazaguanine reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta structure / tunneling fold / reductase / cytosol
Function / homology
Function and homology information


preQ1 synthase / preQ1 synthase activity / queuosine biosynthetic process / cytoplasm
Similarity search - Function
NADPH-dependent 7-cyano-7-deazaguanine reductase, QueF type 2 / NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal / Nitrile reductase, 7-cyano-7-deazaguanine-reductase N-term / NADPH-dependent 7-cyano-7-deazaguanine reductase QueF / QueF-like protein / GTP Cyclohydrolase I, domain 2 / GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
7-DEAZA-7-AMINOMETHYL-GUANINE / NADPH-dependent 7-cyano-7-deazaguanine reductase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKim, Y. / Zhou, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of the C194A mutant of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with preQ1
Authors: Kim, Y. / Zhou, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / CSGID
History
DepositionMay 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH-dependent 7-cyano-7-deazaguanine reductase
B: NADPH-dependent 7-cyano-7-deazaguanine reductase
C: NADPH-dependent 7-cyano-7-deazaguanine reductase
D: NADPH-dependent 7-cyano-7-deazaguanine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,03410
Polymers133,1334
Non-polymers9016
Water8,467470
1
A: NADPH-dependent 7-cyano-7-deazaguanine reductase
B: NADPH-dependent 7-cyano-7-deazaguanine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0175
Polymers66,5672
Non-polymers4503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-2 kcal/mol
Surface area19480 Å2
MethodPISA
2
C: NADPH-dependent 7-cyano-7-deazaguanine reductase
D: NADPH-dependent 7-cyano-7-deazaguanine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0175
Polymers66,5672
Non-polymers4503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-5 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.316, 71.192, 71.463
Angle α, β, γ (deg.)110.43, 119.22, 99.33
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
NADPH-dependent 7-cyano-7-deazaguanine reductase / 7-cyano-7-carbaguanine reductase / NADPH-dependent nitrile oxidoreductase / PreQ(0) reductase


Mass: 33283.262 Da / Num. of mol.: 4 / Mutation: C194A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: N16961 / Gene: queF, VC_0902 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q9KTK0, preQ1 synthase
#2: Chemical
ChemComp-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H9N5O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium acetate, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 68972 / Num. obs: 68972 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 32.69 Å2 / Rsym value: 0.078 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 3394 / Rsym value: 0.37 / % possible all: 93.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: dev_725)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BP1

3bp1


Resolution: 2→35.024 Å / SU ML: 0.51 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3446 5.07 %random
Rwork0.171 ---
all0.174 67907 --
obs0.174 67907 95.66 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.782 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso mean: 43 Å2
Baniso -1Baniso -2Baniso -3
1--4.4282 Å2-6.8809 Å23.7935 Å2
2---5.7593 Å20.3931 Å2
3---10.1875 Å2
Refinement stepCycle: LAST / Resolution: 2→35.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8230 0 64 470 8764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078710
X-RAY DIFFRACTIONf_angle_d1.21711872
X-RAY DIFFRACTIONf_dihedral_angle_d15.7263225
X-RAY DIFFRACTIONf_chiral_restr0.0981270
X-RAY DIFFRACTIONf_plane_restr0.0051589
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2-2.02740.33981500.27282440259091
2.0274-2.05640.29581350.25212556269194
2.0564-2.0870.32341340.24312603273796
2.087-2.11970.30131230.22522620274396
2.1197-2.15440.26391410.21512628276997
2.1544-2.19150.27351280.20792569269797
2.1915-2.23140.28061500.20252626277697
2.2314-2.27430.27511270.19042591271897
2.2743-2.32070.23871380.18732658279697
2.3207-2.37120.25671370.17962629276697
2.3712-2.42630.28131490.1832548279797
2.4263-2.4870.22351420.18232666280897
2.487-2.55420.25551540.17382640279498
2.5542-2.62930.26281440.18862568271297
2.6293-2.71420.27391360.18312675281197
2.7142-2.81110.26241230.18132577270097
2.8111-2.92360.24391410.17822615275697
2.9236-3.05660.21871430.1822594273797
3.0566-3.21770.23631340.16892629276396
3.2177-3.41910.21721390.15612596273596
3.4191-3.68280.20681160.15472543265994
3.6828-4.0530.18331510.14412488263993
4.053-4.63830.15831330.13412427256090
4.6383-5.83940.16571460.14952511265794
5.8394-35.02950.19821320.1752464259691
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5459-1.2385-0.83214.73641.78612.40320.22560.01130.7043-0.49280.1174-0.4806-0.38250.2079-0.28770.2835-0.07140.01850.3353-0.00510.395531.835825.70476.0322
22.4357-1.3198-0.49073.37171.38441.62640.078-0.2390.30420.0175-0.0545-0.1944-0.2690.1378-0.06920.326-0.0775-0.03150.34680.01170.252524.015417.80110.3933
31.5326-0.08710.19361.62550.21020.668-0.0196-0.2510.14650.13170.00030.0193-0.066-0.041-0.01240.2223-0.00030.00650.2864-0.01940.193820.544416.40898.1105
40.73710.13820.89622.09430.3891.1081-0.0361-0.19430.4620.17270.13810.1083-0.2934-0.0248-0.10370.39950.03750.03710.3735-0.06030.57035.649536.22639.0708
51.4321-0.27590.13772.19030.4821.65960.007-0.14850.33480.1193-0.0356-0.0894-0.1652-0.00990.01770.25960.018-0.01370.3043-0.03840.374611.401830.42559.9373
62.5193-2.2515-1.18227.69291.84631.93170.26160.0460.2873-0.8125-0.0262-0.836-0.2318-0.0706-0.12790.3871-0.0383-0.02740.33950.07510.208812.25714.4268-22.7816
71.3931-0.8585-0.4435.04441.35581.2624-0.07550.1027-0.0033-0.27740.08630.0184-0.0165-0.04990.01650.309-0.021-0.0310.31450.0410.28875.825911.7603-13.942
80.8052-0.0455-0.94632.13650.67811.4253-0.02110.03850.2085-0.26090.00310.2796-0.1725-0.0735-0.04770.31820.0176-0.06030.28080.03890.2826.22219.6369-13.7375
92.0309-0.8946-2.39863.46752.93725.53360.1090.49730.1289-0.305-0.08940.4089-0.3012-0.83470.01140.35250.0633-0.09350.43580.08840.3841-0.994119.6948-17.1336
100.6580.15530.75210.65060.35864.5559-0.0468-0.00330.14550.1492-0.17610.13470.4346-0.59060.19130.2937-0.0232-0.02430.3805-0.010.3973-1.202514.182-8.0764
112.2448-1.713-1.25851.9440.75670.9424-0.0742-0.0378-0.25850.22960.07930.04910.07680.10510.10590.3454-0.01870.00940.3049-0.03850.448514.5755-3.79863.0567
122.3365-0.2562-0.48741.82710.46311.5023-0.25290.3467-0.4389-0.07360.106-0.33050.31480.0350.14070.31150.03090.03750.27760.0210.394620.4125-12.7621-8.644
130.1699-0.22710.18750.43-0.12190.6834-0.10370.1258-0.0066-0.5706-0.0965-0.3537-0.31980.04370.11430.3316-0.00770.03350.26770.01950.354418.23330.1732-7.6268
141.103-0.7910.57732.4223-0.50231.1218-0.08170.2005-0.0971-0.3630.0702-0.34540.13160.03220.04680.30010.01460.04460.32020.00640.292119.2663-6.2073-12.0245
150.9469-0.22330.23622.84981.39441.4822-0.1312-0.1106-0.04240.2678-0.09540.17960.1735-0.14970.24740.2567-0.01190.01630.30310.01880.26348.51011.1215-7.8947
161.58330.85761.23114.49294.41568.02330.0342-0.08720.0508-0.0188-0.49680.47880.2178-0.53460.30250.27640.0532-0.07030.30310.01760.4246-29.19120.3175-2.7942
170.39630.37530.11991.33680.91832.34820.1750.04790.09380.0538-0.0824-0.01550.0165-0.1631-0.0010.30560.01390.0040.29330.03740.3239-18.25982.1897-0.7212
180.7912-0.0991-0.47670.99071.00721.2187-0.19620.101-0.0651-0.4024-0.01220.2446-0.0416-0.02840.12940.3262-0.014-0.06880.2760.03130.2394-21.4318-7.2648-11.2699
194.5287-3.1605-2.15375.27612.86943.27520.21410.75650.1068-0.6302-0.19810.1138-0.4738-0.20380.10610.39730.0052-0.07870.40330.0620.2579-21.011-0.8985-15.817
201.7604-1.15210.28172.4033-0.21190.32720.11620.10510.328-0.46980.1098-0.5003-0.03370.1079-0.18210.3445-0.03030.01920.3857-0.00340.3458-8.6889-4.8352-9.3426
212.1268-0.1078-0.29461.25980.73673.11610.0836-0.24580.16220.12460.08630.1690.08870.0836-0.09910.3371-0.0595-0.00430.3588-0.04040.3444-9.1464-4.174621.0006
222.2446-0.3509-0.52310.38710.00120.6429-0.0343-0.23760.23140.018-0.00070.2851-0.126-0.0019-0.12550.3124-0.05520.03760.3647-0.04450.312-11.87831.870718.3487
231.30710.91110.65521.50070.67031.49590.0371-0.220.26360.1104-0.01360.2034-0.079-0.0647-0.04930.25060.01490.01940.3151-0.00330.2883-14.193.341816.1295
240.5433-0.323-0.01544.03781.85641.77490.05830.0040.1951-0.0940.1215-0.5141-0.07680.1749-0.18370.2586-0.00170.02980.29730.03050.2796-10.42680.81064.7613
252.12690.8018-0.16644.45813.5157.5056-0.16810.0572-0.13740.2084-0.38270.64720.538-0.88410.58890.2918-0.04890.02720.33630.01210.4113-22.3786-32.65679.1129
260.9611-0.3944-0.60672.341.0313.3615-0.06390.0451-0.218-0.0279-0.12410.14240.2263-0.05990.10260.2629-0.0066-0.02520.26330.04110.3183-11.4364-27.85338.1448
270.88320.3333-0.34092.04790.68112.1519-0.0682-0.0307-0.15530.1724-0.01030.03010.20110.14730.03490.30840.01890.00960.29610.05830.2379-13.341-25.914415.0456
280.8690.358-0.91341.6365-1.19671.42860.0548-0.1242-0.07110.0244-0.1589-0.40720.00370.3050.0340.30970.0228-0.00550.38070.020.3942-2.9188-21.76499.0171
291.96080.44880.88761.98250.14842.1728-0.10620.30130.2204-0.7080.05030.12220.12270.07940.03570.5882-0.02640.05250.4046-0.02860.3183-12.3879-23.664-19.6994
303.130.38391.01252.8804-0.35421.20750.06610.4447-0.3295-0.4352-0.0043-0.18910.20240.08030.00690.4618-0.01660.07120.372-0.02440.3528-10.8859-31.3341-18.4804
311.4442-0.2048-0.04172.11440.26132.2503-0.00370.1658-0.284-0.39380.01170.02630.3268-0.0449-0.01830.4467-0.06420.02330.3028-0.01540.2659-13.9716-32.3109-14.13
321.77130.0781-0.19593.049-0.08432.544-0.00520.0247-0.1368-0.1066-0.0267-0.39180.19840.22180.02330.30640.00970.0090.32940.01660.2266-7.2385-28.0896-4.1055
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 29:48)
2X-RAY DIFFRACTION2chain 'A' and (resseq 49:75)
3X-RAY DIFFRACTION3chain 'A' and (resseq 76:167)
4X-RAY DIFFRACTION4chain 'A' and (resseq 168:200)
5X-RAY DIFFRACTION5chain 'A' and (resseq 201:287)
6X-RAY DIFFRACTION6chain 'B' and (resseq 29:47)
7X-RAY DIFFRACTION7chain 'B' and (resseq 48:75)
8X-RAY DIFFRACTION8chain 'B' and (resseq 76:112)
9X-RAY DIFFRACTION9chain 'B' and (resseq 113:128)
10X-RAY DIFFRACTION10chain 'B' and (resseq 129:142)
11X-RAY DIFFRACTION11chain 'B' and (resseq 143:162)
12X-RAY DIFFRACTION12chain 'B' and (resseq 163:187)
13X-RAY DIFFRACTION13chain 'B' and (resseq 188:212)
14X-RAY DIFFRACTION14chain 'B' and (resseq 213:248)
15X-RAY DIFFRACTION15chain 'B' and (resseq 249:287)
16X-RAY DIFFRACTION16chain 'C' and (resseq 29:47)
17X-RAY DIFFRACTION17chain 'C' and (resseq 48:70)
18X-RAY DIFFRACTION18chain 'C' and (resseq 71:112)
19X-RAY DIFFRACTION19chain 'C' and (resseq 113:128)
20X-RAY DIFFRACTION20chain 'C' and (resseq 129:147)
21X-RAY DIFFRACTION21chain 'C' and (resseq 148:167)
22X-RAY DIFFRACTION22chain 'C' and (resseq 168:200)
23X-RAY DIFFRACTION23chain 'C' and (resseq 201:248)
24X-RAY DIFFRACTION24chain 'C' and (resseq 249:287)
25X-RAY DIFFRACTION25chain 'D' and (resseq 27:48)
26X-RAY DIFFRACTION26chain 'D' and (resseq 49:75)
27X-RAY DIFFRACTION27chain 'D' and (resseq 76:128)
28X-RAY DIFFRACTION28chain 'D' and (resseq 129:147)
29X-RAY DIFFRACTION29chain 'D' and (resseq 148:167)
30X-RAY DIFFRACTION30chain 'D' and (resseq 168:200)
31X-RAY DIFFRACTION31chain 'D' and (resseq 201:248)
32X-RAY DIFFRACTION32chain 'D' and (resseq 249:287)

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